#!/bin/sh

#  0_preparation.sh
#  
#
#

### Log in to metacentrum ###

ssh user@skirit.ics.muni.cz

## your home directory on skirit front end is brno2/home/username/
##!!! IMPORTANT !!! If you logged in another  front end, the home directory will be different!

#check where you are
pwd

## create your own directory for data and results in the brno2/home/username/ - since we are already there, we operate inside

mkdir -p RNAseq/data/raw
mkdir -p RNAseq/scripts
mkdir -p RNAseq/results/qc

## copy example data to the data/raw
ls -l /storage/brno11-elixir/home/vaclavhejret/Bi5444/RNA-Seq/data/raw/
cp /storage/brno11-elixir/home/vaclavhejret/Bi5444/RNA-Seq/data/raw/*.fastq.gz RNAseq/data/raw/.

## copy the file with known adapters
cp /storage/brno11-elixir/home/vaclavhejret/Bi5444/RNA-Seq/adapters_merge.txt RNAseq/data/raw/.

## open the script 01_initial_qc.sh




